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RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities.

Pommier T, Canbäck B, Lundberg P, Hagström A, Tunlid A - Bioinformatics (2009)

Bottom Line: An ease-of-use web application for this purpose has been missing.We have developed RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance.RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly.

View Article: PubMed Central - PubMed

Affiliation: Department of Natural Science, Kalmar University, Kalmar, Sweden. tpommier@univ-montp2.fr

ABSTRACT

Motivation: The most common approach to estimate microbial diversity is based on the analysis of DNA sequences of specific target genes including ribosomal genes. Commonly, the sequences are grouped into operational taxonomic units based on genetic distance (sequence similarity) instead of genetic change (patristic distance). This method may fail to adequately identify clusters of evolutionary related sequences and it provides no information on the phylogenetic structure of the community. An ease-of-use web application for this purpose has been missing.

Results: We have developed RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly.

Availability: RAMI is licensed under GNU GPL and can be run or downloaded from http://www.acgt.se/online.html.

Supplementary information: http://www.acgt.se/RAMI/SuppInfo.

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Explanation of indices produced by RAMI. (a) RAMI produces indices that describe properties within sequence clusters: Xdepth,nearest, Xdepth,deepest and Xdistance. With a single sequence cluster, all indices will have a value of 0. (b) Analogous, the corresponding properties are measured between sequence clusters with the Ydepth,nearest, Ydepth,deepest and Ydistance indices. The value of Ydepth,deepest is dependent on the choice of outgroup. RAMI has the option to remove outgroup sequences from the analysis, which is important to get a proper value of the Ydistance index. Note that cluster 1 is paraphyletic.
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Figure 2: Explanation of indices produced by RAMI. (a) RAMI produces indices that describe properties within sequence clusters: Xdepth,nearest, Xdepth,deepest and Xdistance. With a single sequence cluster, all indices will have a value of 0. (b) Analogous, the corresponding properties are measured between sequence clusters with the Ydepth,nearest, Ydepth,deepest and Ydistance indices. The value of Ydepth,deepest is dependent on the choice of outgroup. RAMI has the option to remove outgroup sequences from the analysis, which is important to get a proper value of the Ydistance index. Note that cluster 1 is paraphyletic.

Mentions: Available clustering algorithms use genetic distances between sequences to build clusters. The genetic distance is calculated from scores that may be produced in various ways. Patristic distances represent the amount of genetic changes between sequences. In a phylogenetic tree in the form of a phylogram patristic distances correspond to the lengths of the branches. Very few tree reconstruction programs output patristic distance matrices but nearly all have the option to save the tree file in Newick or related formats. RAMI uses such files as input file to calculate the patristic distances between both internal and external nodes. Using a single-linkage algorithm, RAMI then clusters sequences into OTUs that are found within a patristic distance set by the user. Once the clusters are defined, a number of indices are calculated (Fig. 2).Fig. 2.


RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities.

Pommier T, Canbäck B, Lundberg P, Hagström A, Tunlid A - Bioinformatics (2009)

Explanation of indices produced by RAMI. (a) RAMI produces indices that describe properties within sequence clusters: Xdepth,nearest, Xdepth,deepest and Xdistance. With a single sequence cluster, all indices will have a value of 0. (b) Analogous, the corresponding properties are measured between sequence clusters with the Ydepth,nearest, Ydepth,deepest and Ydistance indices. The value of Ydepth,deepest is dependent on the choice of outgroup. RAMI has the option to remove outgroup sequences from the analysis, which is important to get a proper value of the Ydistance index. Note that cluster 1 is paraphyletic.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2654800&req=5

Figure 2: Explanation of indices produced by RAMI. (a) RAMI produces indices that describe properties within sequence clusters: Xdepth,nearest, Xdepth,deepest and Xdistance. With a single sequence cluster, all indices will have a value of 0. (b) Analogous, the corresponding properties are measured between sequence clusters with the Ydepth,nearest, Ydepth,deepest and Ydistance indices. The value of Ydepth,deepest is dependent on the choice of outgroup. RAMI has the option to remove outgroup sequences from the analysis, which is important to get a proper value of the Ydistance index. Note that cluster 1 is paraphyletic.
Mentions: Available clustering algorithms use genetic distances between sequences to build clusters. The genetic distance is calculated from scores that may be produced in various ways. Patristic distances represent the amount of genetic changes between sequences. In a phylogenetic tree in the form of a phylogram patristic distances correspond to the lengths of the branches. Very few tree reconstruction programs output patristic distance matrices but nearly all have the option to save the tree file in Newick or related formats. RAMI uses such files as input file to calculate the patristic distances between both internal and external nodes. Using a single-linkage algorithm, RAMI then clusters sequences into OTUs that are found within a patristic distance set by the user. Once the clusters are defined, a number of indices are calculated (Fig. 2).Fig. 2.

Bottom Line: An ease-of-use web application for this purpose has been missing.We have developed RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance.RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly.

View Article: PubMed Central - PubMed

Affiliation: Department of Natural Science, Kalmar University, Kalmar, Sweden. tpommier@univ-montp2.fr

ABSTRACT

Motivation: The most common approach to estimate microbial diversity is based on the analysis of DNA sequences of specific target genes including ribosomal genes. Commonly, the sequences are grouped into operational taxonomic units based on genetic distance (sequence similarity) instead of genetic change (patristic distance). This method may fail to adequately identify clusters of evolutionary related sequences and it provides no information on the phylogenetic structure of the community. An ease-of-use web application for this purpose has been missing.

Results: We have developed RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly.

Availability: RAMI is licensed under GNU GPL and can be run or downloaded from http://www.acgt.se/online.html.

Supplementary information: http://www.acgt.se/RAMI/SuppInfo.

Show MeSH